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PDBsum entry 1bnl
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protein metals Protein-protein interface(s) links
Extracellular matrix PDB id
1bnl

 

 

 

 

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Contents
Protein chain
178 a.a. *
Metals
_ZN ×4
* Residue conservation analysis
PDB id:
1bnl
Name: Extracellular matrix
Title: Zinc dependent dimers observed in crystals of human endostatin
Structure: Collagen xviii. Chain: a, b, c, d. Fragment: endostatin, 20-kda collagen xviii c-terminal globular domain. Engineered: yes
Source: Homo sapiens. Human. Organism_taxid: 9606. Cellular_location: secreted. Gene: collagen xviii. Expressed in: ns/0 murine myeloma cells.
Resolution:
2.90Å     R-factor:   0.240     R-free:   0.275
Authors: Y.-H.Ding,K.Javaherian,K.-M.Lo,R.Chopra,T.Boehm,J.Lanciotti, B.A.Harris,Y.Li,R.Shapiro,E.Hohenester,R.Timpl,J.Folkman,D.C.Wiley
Key ref:
Y.H.Ding et al. (1998). Zinc-dependent dimers observed in crystals of human endostatin. Proc Natl Acad Sci U S A, 95, 10443-10448. PubMed id: 9724722 DOI: 10.1073/pnas.95.18.10443
Date:
30-Jul-98     Release date:   14-Oct-98    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
P39060  (COIA1_HUMAN) -  Collagen alpha-1(XVIII) chain from Homo sapiens
Seq:
Struc: 		 
Seq:
Struc: 		 
Seq:
Struc: 		 
Seq:
Struc: 		1754 a.a.
178 a.a.*
Key:    Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 

 
DOI no: 10.1073/pnas.95.18.10443 Proc Natl Acad Sci U S A 95:10443-10448 (1998)
PubMed id: 9724722  
 
 
Zinc-dependent dimers observed in crystals of human endostatin.
Y.H.Ding, K.Javaherian, K.M.Lo, R.Chopra, T.Boehm, J.Lanciotti, B.A.Harris, Y.Li, R.Shapiro, E.Hohenester, R.Timpl, J.Folkman, D.C.Wiley.
 
  ABSTRACT  
 
The crystal structure of human endostatin reveals a zinc-binding site. Atomic absorption spectroscopy indicates that zinc is a constituent of both human and murine endostatin in solution. The human endostatin zinc site is formed by three histidines at the N terminus, residues 1, 3, and, 11, and an aspartic acid at residue 76. The N-terminal loop ordered around the zinc makes a dimeric contact in human endostatin crystals. The location of the zinc site at the amino terminus, immediately adjacent to the precursor cleavage site, suggests the possibility that the zinc may be involved in activation of the antiangiogenic activity following cleavage from the inactive collagen XVIII precursor or in the cleavage process itself.
 
  Selected figure(s)  
 
Figure 1.
Fig. 1. The structure of human endostatin. -strands (cyan) are labeled in sequential order A-P, helices are violet, and connecting loops are pink. Residues 1-6 are blue; zinc is a black circle. Human and murine endostatin are very similar (rms deviation = 0.46 Å for 196 C pairs; cf. Fig. 3B in ref. 3). 		Figure 4.
Fig. 4. A positively charged surface formed by arginines on the human endostatin dimer. Stereo diagram, surface glutamines (yellow), asparagines (cyan), lysines (green), and arginines (blue) are shown.
 
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20535417 L.D.D'Andrea, A.Romanelli, R.Di Stasi, and C.Pedone (2010).
Bioinorganic aspects of angiogenesis.
  Dalton Trans, 39, 7625-7636.  
19901987 W.Farrugia, A.M.Scott, and P.A.Ramsland (2009).
A possible role for metallic ions in the carbohydrate cluster recognition displayed by a lewis y specific antibody.
  PLoS One, 4, e7777.
PDB code: 3eyv
19472178 Y.Fu, H.Tang, Y.Huang, N.Song, and Y.Luo (2009).
Unraveling the mysteries of endostatin.
  IUBMB Life, 61, 613-626.  
17447877 A.V.Digtyar, N.V.Pozdnyakova, N.B.Feldman, S.V.Lutsenko, and S.E.Severin (2007).
Endostatin: current concepts about its biological role and mechanisms of action.
  Biochemistry (Mosc), 72, 235-246.  
16409133 J.Folkman (2006).
Angiogenesis.
  Annu Rev Med, 57, 1.  
16456550 R.M.Tjin Tham Sjin, J.Naspinski, A.E.Birsner, C.Li, R.Chan, K.M.Lo, S.Gillies, D.Zurakowski, J.Folkman, J.Samulski, and K.Javaherian (2006).
Endostatin therapy reveals a U-shaped curve for antitumor activity.
  Cancer Gene Ther, 13, 619-627.  
16804605 S.Pieraccini, M.Sironi, P.Francescato, G.Speranza, L.M.Vicentini, and P.Manitto (2006).
A molecular dynamics study of human endostatin and its synthetic fragments with antiangiogenic properties.
  Phys Chem Chem Phys, 8, 3066-3071.  
16869777 M.A.Grant, and R.Kalluri (2005).
Structural basis for the functions of endogenous angiogenesis inhibitors.
  Cold Spring Harb Symp Quant Biol, 70, 399-410.  
16115201 S.Stahl, S.Gaetzner, T.D.Mueller, and U.Felbor (2005).
Endostatin phenylalanines 31 and 34 define a receptor binding site.
  Genes Cells, 10, 929-939.  
15036262 S.Pasco, L.Ramont, F.X.Maquart, and J.C.Monboisse (2004).
Control of melanoma progression by various matrikines from basement membrane macromolecules.
  Crit Rev Oncol Hematol, 49, 221-233.  
12657135 D.R.Sorensen, and T.A.Read (2002).
Delivery of endostatin in experimental cancer therapy.
  Int J Exp Pathol, 83, 265-274.  
12196635 J.C.Zhang, F.Donate, X.Qi, N.P.Ziats, J.C.Juarez, A.P.Mazar, Y.P.Pang, and K.R.McCrae (2002).
The antiangiogenic activity of cleaved high molecular weight kininogen is mediated through binding to endothelial cell tropomyosin.
  Proc Natl Acad Sci U S A, 99, 12224-12229.  
12376553 N.Ortega, and Z.Werb (2002).
New functional roles for non-collagenous domains of basement membrane collagens.
  J Cell Sci, 115, 4201-4214.  
11257123 C.J.Kuo, K.R.LaMontagne, G.Garcia-Cardeña, B.D.Ackley, D.Kalman, S.Park, R.Christofferson, J.Kamihara, Y.H.Ding, K.M.Lo, S.Gillies, J.Folkman, R.C.Mulligan, and K.Javaherian (2001).
Oligomerization-dependent regulation of motility and morphogenesis by the collagen XVIII NC1/endostatin domain.
  J Cell Biol, 152, 1233-1246.  
11177745 R.S.Herbst, A.T.Lee, H.T.Tran, and J.L.Abbruzzese (2001).
Clinical studies of angiogenesis inhibitors: the University of Texas MD Anderson Center Trial of Human Endostatin.
  Curr Oncol Rep, 3, 131-140.  
11020798 C.T.Chen, J.Lin, Q.Li, S.S.Phipps, J.L.Jakubczak, D.A.Stewart, Y.Skripchenko, S.Forry-Schaudies, J.Wood, C.Schnell, and P.L.Hallenbeck (2000).
Antiangiogenic gene therapy for cancer via systemic administration of adenoviral vectors expressing secretable endostatin.
  Hum Gene Ther, 11, 1983-1996.  
10813833 H.Zhang, K.Huang, Z.Li, L.Banerjei, K.E.Fisher, N.V.Grishin, E.Eisenstein, and O.Herzberg (2000).
Crystal structure of YbaK protein from Haemophilus influenzae (HI1434) at 1.8 A resolution: functional implications.
  Proteins, 40, 86-97.
PDB codes: 1dbu 1dbx
10885579 U.K.Zatterstrom, U.Felbor, N.Fukai, and B.R.Olsen (2000).
Collagen XVIII/endostatin structure and functional role in angiogenesis.
  Cell Struct Funct, 25, 97.  
10449407 N.Yamaguchi, B.Anand-Apte, M.Lee, T.Sasaki, N.Fukai, R.Shapiro, I.Que, C.Lowik, R.Timpl, and B.R.Olsen (1999).
Endostatin inhibits VEGF-induced endothelial cell migration and tumor growth independently of zinc binding.
  EMBO J, 18, 4414-4423.  
10562536 T.Sasaki, H.Larsson, J.Kreuger, M.Salmivirta, L.Claesson-Welsh, U.Lindahl, E.Hohenester, and R.Timpl (1999).
Structural basis and potential role of heparin/heparan sulfate binding to the angiogenesis inhibitor endostatin.
  EMBO J, 18, 6240-6248.  
  10393839 Z.Chang, A.Choon, and A.Friedl (1999).
Endostatin binds to blood vessels in situ independent of heparan sulfate and does not compete for fibroblast growth factor-2 binding.
  Am J Pathol, 155, 71-76.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB code is shown on the right.

 

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